Do you mean that when you copy a save from your computer onto the G6 the old save is still there afterwards? If so, the solution is to start up the G6 in the DS and let it process the save data before copying saves to or from the G6.

It stores the save in the RAM, so that next time you boot up your DS it will write the save to the hard drive. This is a pretty good alternative to live saves, but if your battery dies you will lose the save, if your battery loses the ability to charge then you will have to software reset everytime before you turn off your DS in order to save the game. (I know this isn't what your talking about but if someone has a problem similar to this they may search this thread)